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14,866 results for “cancer cell”
Aberrant super-enhancer landscape in enzalutamide-resistant prostate cancer cells
GEO Series GSE228308. Homo sapiens. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Expression analysis of Human esophagus cancer cell line TE-1 transfected with PCDNA3.1 and PCDNA3.1-Pax2
GEO Series GSE64093. Homo sapiens. 2 samples. Type: Expression profiling by array.
Signalling networks govern immune cell avoidance in colorectal cancer
<p>Please refer to https://doi.org/10.5281/zenodo.7015015 instead!</p>
Ovarian cancer is detectable from peripheral blood using machine learning over T cell repertoires
<p>To see if TCR repertoire obtained from peripheral blood is associated with tumor status, we collected blood samples from 85 women with or without ovarian cancer and produced T cell receptor information. Using machine learning, we stratified, with high success rates, the two groups, thereby associating peripheral blood T cell repertoire with the existence of ovarian cancer tumors.</p>
Multi-omic profiling highlights factors associated with resistance to immuno-chemotherapy in non-small cell lung cancer
<p>Processed bulk RNA-seq, spatial transcriptomics and scRNA-seq dataset of NSCLC related to the article “Multi-omic profiling highlights factors associated with resistance to immuno-chemotherapy in non-small cell lung cancer”.</p> <p><strong>Application Requirements for Data Access</strong></p> <p>To apply for access to this dataset, applicants might adhere to the following conditions:</p> <ol> <li> <p><strong>Academic Institution Email</strong>: Applicants are required to use an official email address associated with a recognized academic institution.</p> </li> <li> <p><strong>Identification of Affiliation and Name</strong>: Applicants might provide their full name and clearly state their institutional affiliation, including the department or unit.</p> </li> <li> <p><strong>Usage Commitment</strong>: Applicants must agree not to distribute the data to third parties or use it for commercial purposes. The data is to be used solely for academic and research activities.</p> </li> </ol> <p> </p>
Dataset related to the article "Single- cell profiling defines the prognostic benefit of CD39hi tissue resident memory CD8+ T cells in lumina-like breast cancer"
<p>This record contains data related to the article " Single- cell profiling defines the prognostic benefit of CD39hi tissue resident memory CD8+ T cells in lumina-like breast cancer ".</p> <p>Luminal-like breast cancer (BC) constitutes the majority of BC subtypes, but, differently from highly aggressive triple negative BC, is poorly infiltrated by the immune system. The quality of the immune infiltrate in luminal-like BCs has been poorly studied, thereby limiting further investigation of immunotherapeutic strategies. By using high-dimensional single-cell technologies, we identify heterogeneous behavior within the tissue-resident memory CD8+ T (Trm) cells infiltrating luminal-like tumors. A subset of CD127- CD39<sup>hi</sup> Trm cells, preferentially present in the tumor compared to the adjacent normal breast tissue or peripheral blood, retains enhanced degranulation capacity compared to the CD127+ CD39<sup>lo</sup> Trm counterpart ex vivo, and is specifically associated with positive prognosis. Nevertheless, such prognostic benefit is lost in the presence of highly-suppressive CCR8<sup>hi</sup> ICOS<sup>hi</sup> IRF4+ effector Tregs. Thus, combinatorial strategies aiming at boosting Trm function and infiltration while relieving from Treg-mediated immunosuppression should be investigated to achieve proper tumor control in luminal-like BCs.</p> <p> </p>
Dataset related to article "Mitochondrial metabolic reprogramming controls the induction of immunogenic cell death and efficacy of chemotherapy in bladder cancer "
<p>This record contains raw data related to article “Mitochondrial metabolic reprogramming controls the induction of immunogenic cell death and efficacy of chemotherapy in bladder cancer"</p> <p>Although chemotherapeutic agents have been used for decades, the mechanisms of action, mechanisms of resistance, and the best treatment schedule remain elusive. Mitomycin C (MMC) is the gold standard treatment for non-muscle-invasive bladder cancer (NMIBC). However, it is effective only in a subset of patients, suggesting that, aside from cytotoxicity, other mechanisms could be involved in mediating the success of the treatment. Here, we showed that MMC promotes immunogenic cell death (ICD) and in vivo tumor protection. MMC-induced ICD relied on metabolic reprogramming of tumor cells toward increased oxidative phosphorylation. This favored increased mitochondrial permeability leading to the cytoplasmic release of mitochondrial DNA, which activated the inflammasome for efficient IL-1β (interleukin-1β) secretion that promoted dendritic cell maturation. Resistance to ICD was associated with mitochondrial dysfunction related to low abundance of complex I of the respiratory chain. Analysis of complex I in patient tumors indicated that low abundance of this mitochondrial complex was associated with recurrence incidence after chemotherapy in patients with NMIBC. The identification of mitochondria-mediated ICD as a mechanism of action of MMC offers opportunities to optimize bladder cancer management and provides potential markers of treatment efficacy that could be used for patient stratification.</p>
Dataset related to article "Subpopulations of Circulating Cells with Morphological Features of Malignancy Are Preoperatively Detected and Have Differential Prognostic Significance in Non-Small Cell Lung Cancer "
<p>This record contains raw data related to article “Subpopulations of Circulating Cells with Morphological Features of Malignancy Are Preoperatively Detected and Have Differential Prognostic Significance in Non-Small Cell Lung Cancer"</p> <p><strong>Background: </strong> Non-small cell lung cancer (NSCLC) frequently presents when surgical intervention is no longer feasible. Despite local treatment with curative intent, patients might experience disease recurrence. In this context, accurate non-invasive biomarkers are urgently needed. We report the results of a pilot study on the diagnostic and prognostic role of circulating tumor cells (CTCs) in operable NSCLC.</p> <p><strong>Methods: </strong> Blood samples collected from healthy volunteers (<em>n</em> = 10), nodule-negative high-risk individuals enrolled in a screening program (<em>n</em> = 7), and NSCLC patients (<em>n</em> = 74) before surgery were analyzed (4 mL) for the presence of cells with morphological features of malignancy enriched through the ISET<sup>®</sup> technology.</p> <p><strong>Results: </strong> CTC detection was 60% in patients, while no target cells were found in lung cancer-free donors. We identified single CTCs (sCTC, 46%) and clusters of CTCs and leukocytes (heterotypic clusters, hetCLU, 31%). The prevalence of sCTC (sCTC/4 mL ≥ 2) or the presence of hetCLU predicted the risk of disease recurrence within the cohort of early-stage (I-II, <em>n</em> = 52) or advanced stage cases (III-IVA, <em>n</em> = 22), respectively, while other tumor-related factors did not inform prognosis.</p> <p><strong>Conclusions: </strong> Cancer cell hematogenous dissemination occurs frequently in patients with NSCLC without clinical evidence of distant metastases, laying the foundation for the application of cell-based tests in screening programs. CTC subpopulations are fine prognostic classifiers whose clinical validity should be further investigated in larger studies.</p>
Fast, streamlined fluorescence nanoscopy resolves rearrangements of SNARE and cargo proteins in platelets co-incubated with cancer cells.
<p><strong>This folder contains all raw data underlying the results presented in a manuscript, submitted to </strong><strong><em>Journal of Nanobiotechnology</em></strong><strong>, and entitled:</strong></p> <p> </p> <p><strong>Fast, streamlined fluorescence nanoscopy resolves rearrangements of SNARE and cargo proteins in platelets co-incubated with cancer cells.</strong></p> <p> </p> <p><strong>Authored by:</strong></p> <p>Jan Bergstrand<sup>a,+</sup>, Xinyan Miao<sup>a,+</sup>, Chinmaya Venugopal Srambickal<sup>a,+</sup>, Gert Auer<sup>b</sup>, Jerker Widengren<sup>a,*</sup></p> <p><sup>a</sup> Royal Institute of Technology (KTH), Department of Applied Physics, Experimental Biomolecular Physics, Albanova Univ Center, SE-106 91 Stockholm, Sweden</p> <p><sup>b</sup> Karolinska Institutet, Department of Oncology-Pathology, K7, Z1:00, Karolinska University Hospital, 171 76 Stockholm, Sweden</p> <p><sup>* </sup>To whom correspondence should be addressed. E-mail: <a href="mailto:jwideng@kth.se">jwideng@kth.se</a>, Phone: +46-8-7907813</p> <p><sup>+ </sup>These authors contributed equally</p> <p> </p> <p><strong>The data files are grouped into the different </strong><strong>figures where they are presented</strong><strong>.</strong></p> <p> </p> <p><strong>ABSTRACT</strong></p> <p>Background:</p> <p>Increasing evidence suggests that platelets play a central role in cancer progression, with altered storage and selective release from platelets of specific tumor-promoting proteins as a major mechanism. Fluorescence-based super-resolution microscopy (SRM) can resolve nanoscale spatial distribution patterns of such proteins, and how they are altered in platelets upon different activations. Analysing such alterations by SRM thus represents a promising, minimally invasive strategy for platelet-based diagnosis and monitoring of cancer progression. However, broader applicability beyond specialized research labs will require objective, more automated imaging procedures. Moreover, for statistically significant analyses many SRM platelet images are needed, of several different platelet proteins. Such proteins, showing alterations in their distributions upon cancer progression additionally need to be identified.</p> <p>Results:</p> <p>A fast, streamlined and objective procedure for SRM platelet image acquisition, analysis and classification was developed to overcome these limitations. By stimulated emission depletion SRM we imaged nanoscale patterns of six different platelet proteins; four different SNAREs (soluble N-ethylmaleimide factor attachment protein receptors) mediating protein secretion by membrane fusion of storage granules, and two angiogenesis regulating proteins, representing cargo proteins within these granules coupled to tumor progression. By an streamlined procedure, we recorded about 100 SRM images of platelets, for each of these six proteins, and for five different categories of platelets; incubated with cancer cells (MCF-7, MDA-MB-231, EFO-21), non-cancer cells (MCF-10A), or no cells at all. From these images, structural similarity and protein cluster parameters were determined, and probability functions of these parameters were generated for the different platelet categories. By comparing these probability functions between the categories, we could identify nanoscale alterations in the protein distributions, allowing us to classify the platelets into their correct categories, if they were co-incubated with cancer cells, non-cancer cells, or no cells at all.</p> <p>Conclusions:</p> <p>The fast, streamlined and objective acquisition and analysis procedure established in this work confirms the role of SNAREs and angiogenesis-regulating proteins in platelet-mediated cancer progression, provides additional fundamental knowledge on the interplay between tumor cells and platelets, and represent an important step towards using tumor-platelet interactions and redistribution of nanoscale protein patterns in platelets as a basis for cancer diagnostics.</p> <p> </p> <p><strong>Key Words:</strong></p> <p>STED, super-resolution microscopy, platelet, cancer, tumorigenesis, SNARE protein, dictionary learning</p>
Dataset related to article "Tumor heterogeneity, hypoxia, and immune markers in surgically resected non-small-cell lung cancer"
<p>This record contains raw data related to article "Tumor heterogeneity, hypoxia, and immune markers in surgically resected non-small-cell lung cancer"</p> <p>OBJECTIVES:</p> <p>This study aimed to determine the prognostic role of textural features and their association with metabolic parameters, hypoxia, and cancer-related immune markers in non-small-cell lung cancer (NSCLC) patients.</p> <p>PATIENTS AND METHODS:</p> <p>The trial was registered at http://www.clinicaltrials.gov (<a href="http://clinicaltrials.gov/show/NCT02519062">NCT02519062</a>). From January 2010 to May 2014, 44 patients (male : female=33 : 11; median age: 69.5 years), referred to our Institution for NSCLC resection, were enrolled. Tumor specimens were assessed for HIF-1α, CD68-TAMs, CD8-TILs, PD-1-TILs, and PD-L1 expressions. All patients underwent fluorine-18-fluorodeoxyglucose (F-FDG) PET before surgery. Semiquantitative parameters included maximum standardized uptake value (SUVmax), SUVpeak, SUVmean, metabolic tumor volume, and total lesion glycolysis, whereas for heterogeneity, we considered tumor sphericity, skewness, kurtosis, entropy, and energy. Parameters were correlated with disease-free survival (DFS) considering a median follow-up of 22.7 months.</p> <p>RESULTS:</p> <p>SUVmax (cutoff: 7.9; P=0.015), SUVpeak (cutoff: 6.7; P=0.013), SUVmean (cutoff: 5.5; P=0.028), metabolic tumor volume (cutoff: 3.6 cm; P=0.027), and entropy (cutoff: 1.89; P=0.045) showed a statistically significant association with DFS. Also, a high expression of cytoplasmic HIF-1α (score 3) was associated with DFS (hazard ratio: 0.09; P=0.003). All F-FDG PET variables differed significantly in tumors with high or low entropy (≤1.89). Also, a significantly higher level of mean CD8-TILs was observed in tumors with higher entropy (P=0.041).Using identified prognostic factors, we developed a scoring system, which was confirmed to be associated with DFS (P<0.004). On receiver operating characteristics analysis, a score above 3 was defined as the optimal cutoff point.</p> <p>CONCLUSION:</p> <p>Tumor heterogeneity, metabolic parameters, and high expression of hypoxia were found to be prognostic factors in NSCLC patients who were candidates for surgery. Higher levels of entropy appear to be associated with increased density of CD8-TILs. The combination of investigated prognostic factors enabled the development of a potential scoring system associated with DFS</p>
Inference of tumor cell-specific transcription factor binding from cell-free DNA enables tumor subtype prediction and early detection of cancer
<p>Deregulation of transcription factors (TFs) is an important driver of tumorigenesis. We developed and validated a minimally invasive method for assessing TF activity based on cell-free DNA sequencing and nucleosome footprint analysis. We analyzed whole genome sequencing data for >1,000 cell-free DNA samples from cancer patients and healthy controls using a newly developed bioinformatics pipeline that infers accessibility of TF binding sites from cell-free DNA fragmentation patterns. We observed patient-specific as well as tumor-specific patterns, including accurate prediction of tumor subtypes in prostate cancer, with important clinical implications for the management of patients. Furthermore, we show that cell-free DNA TF profiling is capable of early detection of colorectal carcinomas. Our approach for mapping tumor-specific transcription factor binding <em>in vivo</em> based on blood samples makes a key part of the noncoding genome amenable to clinical analysis</p> <p>This dataset comprises genome-wide midpoint coverages across the early stage colon cancer cohort and non-cancer controls. For every TF and every sample, coverage values relative to the transcription factor binding site are specified ni tab-separated values (one file per sample, one line per TF)</p>
Dataset related to article "Intrahepatic CD69 + Vδ1 T cells re-circulate in the blood of patients with metastatic colorectal cancer and limit tumor progression"
<p>This record contains raw data related to article “Intrahepatic CD69 + Vδ1 T cells re-circulate in the blood of patients with metastatic colorectal cancer and limit tumor progression"</p> <p>Abstract</p> <p><strong>Background: </strong> More than 50% of all patients with colorectal cancer (CRC) develop liver metastases (CLM), a clinical condition characterized by poor prognosis and lack of reliable prognostic markers. Vδ1 cells are a subset of tissue-resident gamma delta (γδ) T lymphocytes endowed with a broad array of antitumor functions and showing a natural high tropism for the liver. However, little is known about their impact in the clinical outcomes of CLM.</p> <p><strong>Methods: </strong> We isolated human γδ T cells from peripheral blood (PB) and peritumoral (PT) tissue of 93 patients undergone surgical procedures to remove CLM. The phenotype of freshly purified γδ T cells was assessed by multiparametric flow cytometry, the transcriptional profiles by single cell RNA-sequencing, the functional annotations by Gene Ontology enrichment analyses and the clonotype by γδ T cell receptor (TCR)-sequencing.</p> <p><strong>Results: </strong> The microenvironment of CLM is characterized by a heterogeneous immune infiltrate comprising different subsets of γδ tumor-infiltrating lymphocytes (TILs) able to egress the liver and re-circulate in PB. Vδ1 T cells represent the largest population of γδ TILs within the PT compartment of CLM that is greatly enriched in Vδ1 T effector (T<sub>EF</sub>) cells expressing constitutive high levels of CD69. These Vδ1 CD69<sup>+</sup> TILs express a distinct phenotype and transcriptional signature, show high antitumor potential and correlate with better patient clinical outcomes in terms of lower numbers of liver metastatic lesions and longer overall survival (OS). Moreover, intrahepatic CD69<sup>+</sup> Vδ1 TILs can egress CLM tissue to re-circulate in PB, where they retain a phenotype, transcriptional signature and TCR clonal repertoires resembling their liver origin. Importantly, even the increased frequencies of the CD69<sup>+</sup> terminally differentiated (T<sub>EMRA</sub>) Vδ1 cells in PB of patients with CLM significantly correlate with longer OS. The positive prognostic score of high frequencies of CD69<sup>+</sup> T<sub>EMRA</sub> Vδ1 cells in PB is independent from the neoadjuvant chemotherapy and immunotherapy regimens administered to patients with CLM prior surgery.</p> <p><strong>Conclusions: </strong> The enrichment of tissue-resident CD69<sup>+</sup> Vδ1 T<sub>EMRA</sub> cells re-circulating at high frequencies in PB of patients with CLM limits tumor progression and represents a new important clinical tool to either predict the natural history of CLM or develop alternative therapeutic protocols of cellular therapies.</p>
Uncovering prognostic architecture of response to immunotherapy in H. pylori infection associated gastric cancer by single-cell transcriptomic analysis
<p>Most gastric cancer (GC) worldwide is ascribed to<em> Helicobacter pylori </em>(<em>H. pylori</em>) infection, which have a detrimental effect on the immunotherapy efficacy, while the key cell players and molecular mechanism associated with GC immunotherapies were rarely described. Herein, we performed comprehensive single-cell-transcriptome analysis of nine GC with current<em> H. pylori</em>-infection (HpGC), three GC with previous <em>H. pylori</em>-infection (ex-HpGC), six GC without <em>H. pylori</em>-infection (non-HpGC), and six healthy controls (HC). HpGC and ex-HpGC were enriched with VEGFA+ angiogenic-tumor-associated-macrophages (Angio-TAM) and IL11/IL24+ inflammatory CAF (iCAF), importantly, iCAFs promoted tumor angiogenesis and immune suppression by interacting with Angio-TAM through VEGFA/B-VEGFR1 and TIGIT+ suppressive T cells through NECTIN2-TIGIT pathway, which is promising target for cancer immunotherapy. Integrated analysis of scRNA and immunotherapy dataset demonstrated the iCAF abundance and angiogenic signature could predict poor GC immunotherapy outcomes. Together, our results delineated the role of <em>H. pylori</em>-infection in GC development, tumor microenvironment regulation, and immunotherapy response.</p>
EZH2 inhibition results in genome-wide PRC2 redistribution in cancer cell models
GEO Series GSE134136. Homo sapiens. 44 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Expression analysis of breast cancer cell lines SKBR-3 and ZR-75-1 upon treatment of LMO2 overexpression or knocking-down
GEO Series GSE105020. Homo sapiens. 4 samples. Type: Expression profiling by array.
RNA seq of breast cancer cells treated with different concentration gradients of Thapsigargin (TG), Tunicamycin (TM), and FCCP.
GEO Series GSE281194. Homo sapiens. 44 samples. Type: Expression profiling by high throughput sequencing.
Enhanced susceptibility of cancer cells to oncolytic rhabdo-virotherapy by expression of Nodamura virus protein B2 as a suppressor of RNA interference
GEO Series GSE115138. Homo sapiens. 9 samples. Type: Expression profiling by array.
Starving advanced prostate cancer cells by pharmacological gluose deprivation with a resveratrol trimer trans-Gnetin H
GEO Series GSE240104. Homo sapiens; Mus musculus. 24 samples. Type: Expression profiling by high throughput sequencing.
RNA SEQUENCING DATA OF VANCOMYCIN TREATED HTB172 LUNG CANCER CELL LINE AND CONTROL,
GEO Series GSE248676. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
KLF5 controls subtype-independent highly interactive enhancers in pancreatic cancer to regulate cell survival [ChIPseq]
GEO Series GSE309860. Homo sapiens. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.